MA just switched over to all electronic tolls, either EZ Pass or optical recognition of license plate and US Mail bill. So things may have been a bit bogged down at first. A couple of notes:

If you have a rental and don't use the transponder, the bill will still be sent to the registered owner of the car )the rental company) and I'm sure you will still get charged the Plate Pass outrageous daily fees. So the OP was wise to get an EZ Pass!

Position of the transponder is far from critical. We have three cars and two transponders. We've never affixed the transponder to the windshield. We just toss 'em on the dash some place when we take a different car. And only two of the cars are registered. Doesn't matter at all.

EZ Pass works up and down the east coast down to Delaware I think, so it can be useful.